ClinVar Miner

Submissions for variant NM_003482.4(KMT2D):c.3109_3110del (p.Ser1037fs)

dbSNP: rs1555196415
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000524060 SCV000621912 pathogenic not provided 2017-10-19 criteria provided, single submitter clinical testing The c.3109_3110delTC variant in the KMT2D gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The variant causes a frameshift starting with codon Serine 1037, changes this amino acid to a Proline residue, and creates a premature Stop codon at position 30 of the new reading frame, denoted p.Ser1037ProfsX30. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.3109_3110delTC variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.3109_3110delTC as a pathogenic variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV002528291 SCV003335270 pathogenic Kabuki syndrome 2022-03-27 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 453057). This variant has not been reported in the literature in individuals affected with KMT2D-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ser1037Profs*30) in the KMT2D gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in KMT2D are known to be pathogenic (PMID: 22126750).

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